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TRIMSEQ(1e) EMBOSS Manual for Debian TRIMSEQ(1e)

trimseq - Remove unwanted characters from start and end of sequence(s)

trimseq -sequence seqall [-window integer] [-percent float] [-strict boolean] [-star boolean] -left boolean -right boolean -outseq seqoutall

trimseq -help

trimseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Edit" command group(s).

-sequence seqall

-window integer

This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage. Default value: 1

-percent float

This is the threshold of the percentage ambiguity in the window required in order to trim a sequence. Default value: 100.0

-strict boolean

In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z. Default value: N

-star boolean

In protein sequences, trim off not only X's, but also the *'s Default value: N

-left boolean

Default value: Y

-right boolean

Default value: Y

-outseq seqoutall

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

trimseq is fully documented via the tfm(1) system.

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

Wrote the script used to autogenerate this manual page.

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.

05/11/2012 EMBOSS 6.4.0